Query 044925
Match_columns 103
No_of_seqs 114 out of 923
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:07:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044925.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044925hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3449 60S acidic ribosomal p 99.9 1.4E-26 2.9E-31 162.1 6.6 89 12-103 17-112 (112)
2 PTZ00373 60S Acidic ribosomal 99.9 4.1E-25 8.9E-30 155.1 7.0 87 12-103 19-112 (112)
3 PLN00138 large subunit ribosom 99.9 8.3E-25 1.8E-29 153.6 7.1 90 12-103 17-113 (113)
4 cd05833 Ribosomal_P2 Ribosomal 99.9 1.1E-24 2.5E-29 152.0 6.9 92 10-103 14-109 (109)
5 cd04411 Ribosomal_P1_P2_L12p R 99.9 1.7E-24 3.6E-29 150.2 6.9 89 10-102 14-105 (105)
6 cd05831 Ribosomal_P1 Ribosomal 99.9 3.6E-23 7.8E-28 143.0 6.8 90 8-102 13-103 (103)
7 COG2058 RPP1A Ribosomal protei 99.8 2.2E-21 4.8E-26 135.5 6.0 97 6-103 10-109 (109)
8 PF00428 Ribosomal_60s: 60s Ac 99.8 2.8E-21 6.2E-26 129.1 -0.3 87 12-102 1-88 (88)
9 KOG1762 60s acidic ribosomal p 99.8 6.7E-20 1.5E-24 128.9 5.4 82 21-103 15-114 (114)
10 PRK06402 rpl12p 50S ribosomal 99.7 2.7E-17 5.7E-22 114.7 5.4 47 9-56 13-59 (106)
11 cd05832 Ribosomal_L12p Ribosom 99.4 1E-13 2.3E-18 96.7 4.8 47 9-56 13-59 (106)
12 TIGR03685 L21P_arch 50S riboso 99.4 1.4E-13 3E-18 95.6 5.0 47 9-56 13-59 (105)
13 PTZ00135 60S acidic ribosomal 98.6 4.5E-08 9.7E-13 78.5 3.3 18 86-103 293-310 (310)
14 PTZ00240 60S ribosomal protein 97.9 5.4E-06 1.2E-10 67.2 1.5 17 86-102 306-323 (323)
15 cd04411 Ribosomal_P1_P2_L12p R 97.2 0.00027 5.8E-09 49.1 2.5 45 6-61 26-71 (105)
16 COG2058 RPP1A Ribosomal protei 97.2 0.00029 6.2E-09 49.7 2.3 26 21-48 9-34 (109)
17 PRK06402 rpl12p 50S ribosomal 97.1 0.00071 1.5E-08 47.3 4.0 27 21-49 9-35 (106)
18 KOG3449 60S acidic ribosomal p 96.9 0.00072 1.6E-08 47.8 2.4 38 5-47 26-67 (112)
19 cd05831 Ribosomal_P1 Ribosomal 96.6 0.0035 7.5E-08 43.3 4.3 27 21-49 10-36 (103)
20 PRK04019 rplP0 acidic ribosoma 96.5 0.003 6.5E-08 50.9 4.0 38 12-55 254-292 (330)
21 TIGR03685 L21P_arch 50S riboso 96.4 0.002 4.3E-08 44.8 2.0 26 21-48 9-34 (105)
22 cd05832 Ribosomal_L12p Ribosom 96.1 0.0085 1.8E-07 41.9 3.9 26 21-48 9-34 (106)
23 cd05833 Ribosomal_P2 Ribosomal 94.8 0.023 4.9E-07 39.8 2.3 13 29-41 17-29 (109)
24 PLN00138 large subunit ribosom 91.1 0.12 2.6E-06 36.4 1.4 19 29-48 17-35 (113)
25 PTZ00373 60S Acidic ribosomal 89.9 0.24 5.1E-06 35.0 2.0 14 29-42 19-32 (112)
26 PTZ00240 60S ribosomal protein 84.5 0.58 1.2E-05 38.3 1.6 12 29-40 238-249 (323)
27 PF13833 EF-hand_8: EF-hand do 71.4 4.8 0.0001 23.1 2.5 30 12-42 4-34 (54)
28 PF03540 TFIID_30kDa: Transcri 68.7 4.5 9.7E-05 24.9 2.0 39 13-52 3-41 (51)
29 KOG0031 Myosin regulatory ligh 68.5 10 0.00023 28.6 4.3 41 11-52 47-104 (171)
30 KOG1762 60s acidic ribosomal p 68.2 3.1 6.8E-05 29.6 1.4 20 10-30 20-39 (114)
31 PF11116 DUF2624: Protein of u 64.1 9.7 0.00021 25.7 3.1 36 12-48 14-49 (85)
32 PF12169 DNA_pol3_gamma3: DNA 63.5 9.6 0.00021 26.0 3.1 32 13-49 1-32 (143)
33 PF10281 Ish1: Putative stress 51.1 11 0.00024 21.0 1.4 29 12-41 3-33 (38)
34 PF03979 Sigma70_r1_1: Sigma-7 49.1 18 0.00039 23.3 2.4 36 10-48 19-54 (82)
35 PF07308 DUF1456: Protein of u 45.3 23 0.00051 22.6 2.4 28 12-40 13-40 (68)
36 PF07499 RuvA_C: RuvA, C-termi 44.8 58 0.0013 18.8 3.9 34 16-52 4-40 (47)
37 PF03484 B5: tRNA synthetase B 39.0 14 0.00031 23.0 0.7 18 9-26 15-32 (70)
38 COG5126 FRQ1 Ca2+-binding prot 38.1 52 0.0011 24.4 3.7 41 11-52 35-79 (160)
39 PF05788 Orbi_VP1: Orbivirus R 38.1 16 0.00035 34.8 1.1 41 1-42 1116-1166(1301)
40 smart00874 B5 tRNA synthetase 35.2 23 0.00049 21.6 1.2 15 28-42 17-31 (71)
41 PHA02770 hypothetical protein; 34.6 30 0.00065 22.7 1.7 19 34-52 3-21 (81)
42 PF10815 ComZ: ComZ; InterPro 32.8 22 0.00047 22.4 0.8 37 3-42 4-40 (56)
43 cd00051 EFh EF-hand, calcium b 32.8 73 0.0016 16.9 3.0 30 12-42 16-45 (63)
44 cd05031 S-100A10_like S-100A10 32.4 50 0.0011 21.2 2.5 31 11-42 25-60 (94)
45 smart00523 DWA Domain A in dwa 32.1 35 0.00076 23.8 1.8 26 34-59 9-34 (109)
46 PF03575 Peptidase_S51: Peptid 32.1 31 0.00067 24.2 1.6 50 2-53 15-64 (154)
47 cd05027 S-100B S-100B: S-100B 32.0 60 0.0013 21.1 2.9 40 12-52 26-75 (88)
48 COG1460 Uncharacterized protei 27.8 69 0.0015 22.8 2.7 29 13-42 80-108 (114)
49 PRK00994 F420-dependent methyl 26.1 33 0.00071 27.7 0.9 46 2-47 124-170 (277)
50 PRK06770 hypothetical protein; 25.9 65 0.0014 24.6 2.5 25 24-48 89-113 (180)
51 PF00076 RRM_1: RNA recognitio 25.8 59 0.0013 18.5 1.8 22 5-26 2-23 (70)
52 PF03960 ArsC: ArsC family; I 25.7 56 0.0012 21.6 1.9 25 2-26 22-46 (110)
53 PTZ00135 60S acidic ribosomal 25.1 36 0.00078 27.5 1.0 17 84-100 294-310 (310)
54 PF09682 Holin_LLH: Phage holi 25.0 79 0.0017 21.4 2.6 23 17-40 76-98 (108)
55 PRK12402 replication factor C 24.8 1.2E+02 0.0027 23.0 3.9 37 11-51 235-271 (337)
56 COG0317 SpoT Guanosine polypho 24.5 1.1E+02 0.0023 27.9 3.9 42 15-60 488-529 (701)
57 PF13405 EF-hand_6: EF-hand do 24.4 31 0.00067 17.8 0.4 16 11-26 15-31 (31)
58 KOG0027 Calmodulin and related 24.4 97 0.0021 21.4 3.0 41 11-52 23-68 (151)
59 PRK10853 putative reductase; P 24.1 86 0.0019 21.5 2.6 25 2-26 26-50 (118)
60 PF13443 HTH_26: Cro/C1-type H 23.6 1.1E+02 0.0023 17.8 2.7 38 12-51 21-58 (63)
61 smart00803 TAF TATA box bindin 23.5 1.2E+02 0.0026 18.9 3.0 30 12-42 2-32 (65)
62 TIGR00135 gatC glutamyl-tRNA(G 22.2 99 0.0021 20.1 2.5 30 13-43 1-30 (93)
63 PRK00034 gatC aspartyl/glutamy 21.7 1E+02 0.0023 19.9 2.6 31 12-43 2-32 (95)
64 PF09504 RE_Bsp6I: Bsp6I restr 21.4 72 0.0016 24.3 1.9 32 21-52 2-48 (180)
65 COG5126 FRQ1 Ca2+-binding prot 21.1 95 0.002 23.0 2.5 31 12-43 108-138 (160)
66 COG1927 Mtd Coenzyme F420-depe 21.1 51 0.0011 26.4 1.1 46 2-47 124-170 (277)
67 PF09386 ParD: Antitoxin ParD; 21.1 93 0.002 20.8 2.2 24 28-51 6-31 (79)
68 PF02885 Glycos_trans_3N: Glyc 20.9 1.5E+02 0.0033 18.0 3.1 43 10-52 12-56 (66)
69 PF04940 BLUF: Sensors of blue 20.9 70 0.0015 21.1 1.6 24 2-25 3-26 (93)
70 PF03165 MH1: MH1 domain; Int 20.4 84 0.0018 21.5 2.0 26 34-59 4-31 (103)
71 PTZ00184 calmodulin; Provision 20.4 1.1E+02 0.0023 20.0 2.4 30 12-42 100-129 (149)
72 PF03880 DbpA: DbpA RNA bindin 20.1 28 0.00062 21.8 -0.4 28 21-48 38-65 (74)
No 1
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.4e-26 Score=162.08 Aligned_cols=89 Identities=45% Similarity=0.545 Sum_probs=66.2
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhh-------hcCCCCcccccccccccccCCCCccchhhhhh
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYL-------NVGSGGAHLAVAAPAVASSGLGGAALAAAVEE 84 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa-------~v~agg~a~~aaaa~aa~~~~~a~a~~~~~ee 84 (103)
.-+..||++||.+|| +++|.++|+.||+.|+||+|.|||+ ++++||+++++++++++ ++++++....+++
T Consensus 17 ~psa~DikkIl~sVG-~E~d~e~i~~visel~GK~i~ElIA~G~eklAsvpsGGa~~aaa~~aag--gaa~aa~~a~~~e 93 (112)
T KOG3449|consen 17 SPSASDIKKILESVG-AEIDDERINLVLSELKGKDIEELIAAGREKLASVPSGGAVAAAAAPAAG--GAAGAAPAAAKEE 93 (112)
T ss_pred CCCHHHHHHHHHHhC-cccCHHHHHHHHHHhcCCCHHHHHHHhHHHHhcCCCCCccccccCcCCC--CCccCCccchhhh
Confidence 567899999999999 9999999999999999999999995 68877764322221111 1111222223455
Q ss_pred hhcccccccccCCCCCCCC
Q 044925 85 KKEETKEESDDDMGLSLFD 103 (103)
Q Consensus 85 ~keeeeEE~ddDmGFgLFD 103 (103)
+|+||+|||||||||+|||
T Consensus 94 ~keEe~eesddDmgf~lFd 112 (112)
T KOG3449|consen 94 EKEEEKEESDDDMGFGLFD 112 (112)
T ss_pred hhhhhcccccccccccccC
Confidence 5666669999999999998
No 2
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=99.92 E-value=4.1e-25 Score=155.09 Aligned_cols=87 Identities=31% Similarity=0.448 Sum_probs=62.0
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhh-------hcCCCCcccccccccccccCCCCccchhhhhh
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYL-------NVGSGGAHLAVAAPAVASSGLGGAALAAAVEE 84 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa-------~v~agg~a~~aaaa~aa~~~~~a~a~~~~~ee 84 (103)
.+|.+||++||+++| |+++.++++.|++.|+||+|++||+ ++ ||+++++++++++ ++++++.++++++
T Consensus 19 ~pTaddI~kIL~AaG-veVd~~~~~l~~~~L~GKdI~ELIa~G~~kl~sv--gg~~~aa~a~a~~--~~~~~~~~~~~~e 93 (112)
T PTZ00373 19 NPTKKEVKNVLSAVN-ADVEDDVLDNFFKSLEGKTPHELIAAGMKKLQNI--GGGVAAAAAPAAG--AATAGAKAEAKKE 93 (112)
T ss_pred CCCHHHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHHhHHHHhcc--cCccccccccccc--ccccccchhhhhh
Confidence 599999999999999 9999999999999999999999996 35 3322211111111 1112222233444
Q ss_pred hhcccccccccCCCCCCCC
Q 044925 85 KKEETKEESDDDMGLSLFD 103 (103)
Q Consensus 85 ~keeeeEE~ddDmGFgLFD 103 (103)
+|+||+|||||||||||||
T Consensus 94 ~k~ee~ee~ddDmgf~LFd 112 (112)
T PTZ00373 94 EKKEEEEEEEDDLGFSLFG 112 (112)
T ss_pred hcccccccccccccccccC
Confidence 4566777889999999998
No 3
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=99.91 E-value=8.3e-25 Score=153.60 Aligned_cols=90 Identities=37% Similarity=0.430 Sum_probs=64.5
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhh-------hcCCCCcccccccccccccCCCCccchhhhhh
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYL-------NVGSGGAHLAVAAPAVASSGLGGAALAAAVEE 84 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa-------~v~agg~a~~aaaa~aa~~~~~a~a~~~~~ee 84 (103)
.+|.++|++||+++| ++++.++++.++++|+||+|++||+ ++++||+++++++++++ +++++++.++++++
T Consensus 17 ~pta~dI~~IL~AaG-vevd~~~~~~f~~~L~gK~i~eLIa~G~~kl~sv~~gg~aa~a~a~a~~-~~~~~~~~~~~~~e 94 (113)
T PLN00138 17 CPSAEDLKDILGSVG-ADADDDRIELLLSEVKGKDITELIASGREKLASVPSGGGVAVAAAAAPA-AGGAAAPAAEAKKE 94 (113)
T ss_pred CCCHHHHHHHHHHcC-CcccHHHHHHHHHHHcCCCHHHHHHhchhccccCCCCCccccccccccc-cccccccccchhhh
Confidence 599999999999999 9999999999999999999999995 47776653332211111 00111112223334
Q ss_pred hhcccccccccCCCCCCCC
Q 044925 85 KKEETKEESDDDMGLSLFD 103 (103)
Q Consensus 85 ~keeeeEE~ddDmGFgLFD 103 (103)
+|+|++||+||||||||||
T Consensus 95 ~k~e~eeE~ddDmGfgLFd 113 (113)
T PLN00138 95 EKVEEKEESDDDMGFSLFD 113 (113)
T ss_pred hhccccccccccccccccC
Confidence 4456667889999999998
No 4
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=99.91 E-value=1.1e-24 Score=151.96 Aligned_cols=92 Identities=34% Similarity=0.351 Sum_probs=63.4
Q ss_pred cc-cCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhhcCC--CC-cccccccccccccCCCCccchhhhhhh
Q 044925 10 QI-FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLNVGS--GG-AHLAVAAPAVASSGLGGAALAAAVEEK 85 (103)
Q Consensus 10 ~~-~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~v~a--gg-~a~~aaaa~aa~~~~~a~a~~~~~ee~ 85 (103)
++ .+|+++|++||+++| ++|+..++..+++.|+||+|++||++... ++ +++++++++++ +++++++..++++++
T Consensus 14 g~~~pTa~dI~~IL~AaG-veVe~~~~~lf~~~L~GKdi~eLIa~g~~kl~s~~~~~~~aa~a~-~~~a~aa~~~~~e~k 91 (109)
T cd05833 14 GNASPSAADVKKILGSVG-VEVDDEKLNKVISELEGKDVEELIAAGKEKLASVPAGAGGAAPAA-AAAAAAAAAAKKEEK 91 (109)
T ss_pred CCCCCCHHHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHHhHhhhcCCCcccccccccc-ccccccccchhhhhh
Confidence 44 899999999999999 99999999999999999999999986443 21 11111111111 011111112334455
Q ss_pred hcccccccccCCCCCCCC
Q 044925 86 KEETKEESDDDMGLSLFD 103 (103)
Q Consensus 86 keeeeEE~ddDmGFgLFD 103 (103)
|+|++||+||||||||||
T Consensus 92 kee~eee~ddDmGf~LFd 109 (109)
T cd05833 92 KEESEEESDDDMGFGLFD 109 (109)
T ss_pred ccCCccccccccCCCCCC
Confidence 556666679999999998
No 5
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=99.91 E-value=1.7e-24 Score=150.23 Aligned_cols=89 Identities=27% Similarity=0.324 Sum_probs=62.9
Q ss_pred cccCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhhcCCC--C-cccccccccccccCCCCccchhhhhhhh
Q 044925 10 QIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLNVGSG--G-AHLAVAAPAVASSGLGGAALAAAVEEKK 86 (103)
Q Consensus 10 ~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~v~ag--g-~a~~aaaa~aa~~~~~a~a~~~~~ee~k 86 (103)
++.+|.++|++||.++| ++|+.++++.++++|+|++|++||++.... + ++.+++++++ ++++++.+++++++|
T Consensus 14 g~~~ta~~I~~IL~aaG-veVe~~~~~~~~~aLaGk~V~eli~~g~~kl~~~~~~~~a~~~a---~~~~~~~~~~~~e~k 89 (105)
T cd04411 14 GKELTEDKIKELLSAAG-AEIEPERVKLFLSALNGKNIDEVISKGKELMSSQAAAAAAPAAT---AAATAEPAEKAEEAK 89 (105)
T ss_pred CCCCCHHHHHHHHHHcC-CCcCHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCCcccccccc---ccccccchhhhhhhh
Confidence 56699999999999999 999999999999999999999999865431 1 1111111111 111222223444555
Q ss_pred cccccccccCCCCCCC
Q 044925 87 EETKEESDDDMGLSLF 102 (103)
Q Consensus 87 eeeeEE~ddDmGFgLF 102 (103)
+|++||||||||||||
T Consensus 90 ~ee~eE~dddmgf~LF 105 (105)
T cd04411 90 EEEEEEEDEDFGFGLF 105 (105)
T ss_pred cccccccccccCcccC
Confidence 6677888999999999
No 6
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and
Probab=99.88 E-value=3.6e-23 Score=142.96 Aligned_cols=90 Identities=39% Similarity=0.457 Sum_probs=67.2
Q ss_pred cccccCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhhcCCCCcc-cccccccccccCCCCccchhhhhhhh
Q 044925 8 TVQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLNVGSGGAH-LAVAAPAVASSGLGGAALAAAVEEKK 86 (103)
Q Consensus 8 ~~~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~v~agg~a-~~aaaa~aa~~~~~a~a~~~~~ee~k 86 (103)
.-++.+|.++|++||+++| ++++..+++.+++.|+||+|++||++++++|++ +++++++ + ++++..+++++++|
T Consensus 13 d~~~~~Tae~I~~ilkAaG-veve~~~~~~f~~~L~gk~i~elIa~~~~~~~~aap~a~~a-~---~~~~~~~~~~~~kk 87 (103)
T cd05831 13 DDGIEITADNINALLKAAG-VNVEPYWPGLFAKALEGKDIKDLLSNVGGGGGGAAPAAAAA-A---AAAAAAEAKKEEKK 87 (103)
T ss_pred cCCCCCCHHHHHHHHHHcC-CcccHHHHHHHHHHHcCCCHHHHhhcccccccccccccccc-c---cccccccchhhhcc
Confidence 3478899999999999999 999999999999999999999999998765543 2222111 1 11111223345556
Q ss_pred cccccccccCCCCCCC
Q 044925 87 EETKEESDDDMGLSLF 102 (103)
Q Consensus 87 eeeeEE~ddDmGFgLF 102 (103)
++++||+|||||||||
T Consensus 88 ~e~eee~d~dmgfglF 103 (103)
T cd05831 88 EEEEEESDDDMGFGLF 103 (103)
T ss_pred cccccccccccccccC
Confidence 6677778999999999
No 7
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=2.2e-21 Score=135.53 Aligned_cols=97 Identities=31% Similarity=0.338 Sum_probs=67.3
Q ss_pred eecccccCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhhcCCCCcc-cccccccccccCCCCccc--hhhh
Q 044925 6 MDTVQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLNVGSGGAH-LAVAAPAVASSGLGGAAL--AAAV 82 (103)
Q Consensus 6 ~~~~~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~v~agg~a-~~aaaa~aa~~~~~a~a~--~~~~ 82 (103)
+...++++|+++|+++|.++| |+|+..+++.|++.|+||||+++|.+....-++ +++++++++++++.+++. .++.
T Consensus 10 L~~agkei~e~~l~~vl~aaG-veve~~r~k~lvaaLeg~~idE~i~~~~~~~~a~a~a~aaaa~~A~~~~a~~~~ea~e 88 (109)
T COG2058 10 LHLAGKEITEDNLKSVLEAAG-VEVEEARAKALVAALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEAAAEADEAEE 88 (109)
T ss_pred HHHccCcCCHHHHHHHHHHcC-CCccHHHHHHHHHHhcCCCHHHHHHHhcccccccCCcccccccccccccccchhhHHH
Confidence 356789999999999999999 999999999999999999999999876543211 111111110011111111 2223
Q ss_pred hhhhcccccccccCCCCCCCC
Q 044925 83 EEKKEETKEESDDDMGLSLFD 103 (103)
Q Consensus 83 ee~keeeeEE~ddDmGFgLFD 103 (103)
++++++.+||+++||||+|||
T Consensus 89 Ee~eEe~~EE~~~~~lf~LF~ 109 (109)
T COG2058 89 EEKEEEAEEESDDDMLFGLFG 109 (109)
T ss_pred HHhhhchhhcccccchhhccC
Confidence 334556678889999999998
No 8
>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.
Probab=99.80 E-value=2.8e-21 Score=129.07 Aligned_cols=87 Identities=39% Similarity=0.386 Sum_probs=57.6
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhhcCCCCcccccccccccccCCCCccchhhhhhhhcccc-
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLNVGSGGAHLAVAAPAVASSGLGGAALAAAVEEKKEETK- 90 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~v~agg~a~~aaaa~aa~~~~~a~a~~~~~ee~keeee- 90 (103)
.+|+++|.++|.++| +++++.++..++++|+|++|++||++.+.+++++++++++++ ++.++++++++++|++++
T Consensus 1 ~pT~~~i~~vl~aag-~~v~~~~~~~~~~~l~~~~i~~li~~~~~~~~~~aaa~aaa~---aa~~~a~a~~e~kkEeeee 76 (88)
T PF00428_consen 1 EPTAENIKKVLKAAG-VEVEAIWLELFAKALEGKDIKELIANGSAGMAAAAAAAAAAA---AAAAAAAAAEEEKKEEEEE 76 (88)
T ss_dssp S-SCCCHHHHHHHHT-HHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHTTSSH---HHHHHHHHHSTTHHHHT--
T ss_pred CCCHHHHHHHHHHhC-CchhHHHHHHHHHHHcCCcHHHHHhccccccccccccccccc---ccccccccchhcccccccc
Confidence 378999999999999 999999999999999999999999987765321111111100 011111222223333333
Q ss_pred cccccCCCCCCC
Q 044925 91 EESDDDMGLSLF 102 (103)
Q Consensus 91 EE~ddDmGFgLF 102 (103)
||+|+|||||||
T Consensus 77 EEed~dmGf~LF 88 (88)
T PF00428_consen 77 EEEDDDMGFGLF 88 (88)
T ss_dssp SS-SSSSSTTTT
T ss_pred cccccccCcCCC
Confidence 688999999999
No 9
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=99.80 E-value=6.7e-20 Score=128.93 Aligned_cols=82 Identities=44% Similarity=0.570 Sum_probs=57.4
Q ss_pred hhhhcccccccHHHHHHHHH----------------HhcCCChHHHhhhcCCCCccccccccccc-ccCC-CCccchhhh
Q 044925 21 GLVEFSFFTSQPEKIATLIK----------------LFEKRSADELYLNVGSGGAHLAVAAPAVA-SSGL-GGAALAAAV 82 (103)
Q Consensus 21 ~l~~~g~vevdaekI~~li~----------------aL~gk~I~eLIa~v~agg~a~~aaaa~aa-~~~~-~a~a~~~~~ 82 (103)
||.--+ |+|+.+||++|+| +|.+++|.+||+|+++||+++++..++++ ++++ +++++.+++
T Consensus 15 IL~d~~-i~it~dki~tl~kaa~v~ve~~Wp~lfakale~vni~~li~n~gag~~a~a~~~~~~~~aa~~~~aA~~~Ekk 93 (114)
T KOG1762|consen 15 ILHDDE-IEVTADKINTLTKAAGVNVEPYWPGLFAKALEGVNIKELICNVGAGGGALAAGAAAAGGAAAAGGAAAAEEKK 93 (114)
T ss_pred hccccc-eeeehhhhhhHHHhccCcccccchhHHHHHhccCChHHHHHhcccCCccCCCccccccccccccccccchHHH
Confidence 344456 7777788877665 89999999999999987766544322211 1222 233345556
Q ss_pred hhhhcccccccccCCCCCCCC
Q 044925 83 EEKKEETKEESDDDMGLSLFD 103 (103)
Q Consensus 83 ee~keeeeEE~ddDmGFgLFD 103 (103)
++.|+|+.||+||||||||||
T Consensus 94 ~eak~EeseesddDmgfGLfd 114 (114)
T KOG1762|consen 94 EEAKKEESEESDDDMGFGLFD 114 (114)
T ss_pred HHhhhhhhcccccccccCCCC
Confidence 667778889999999999998
No 10
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=99.69 E-value=2.7e-17 Score=114.68 Aligned_cols=47 Identities=9% Similarity=0.099 Sum_probs=44.1
Q ss_pred ccccCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhhcCC
Q 044925 9 VQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLNVGS 56 (103)
Q Consensus 9 ~~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~v~a 56 (103)
-++.||+++|++||+++| ++|+..+++.|+++|+|+||++||.++++
T Consensus 13 ~g~~it~e~I~~IL~AAG-veVee~~~k~~v~aL~GkdIeElI~~a~~ 59 (106)
T PRK06402 13 AGKEINEDNLKKVLEAAG-VEVDEARVKALVAALEDVNIEEAIKKAAA 59 (106)
T ss_pred cCCCCCHHHHHHHHHHcC-CCccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence 356999999999999999 99999999999999999999999988765
No 11
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=99.45 E-value=1e-13 Score=96.66 Aligned_cols=47 Identities=11% Similarity=0.101 Sum_probs=44.3
Q ss_pred ccccCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhhcCC
Q 044925 9 VQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLNVGS 56 (103)
Q Consensus 9 ~~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~v~a 56 (103)
-++.||+++|++||+++| |+++..+++.|++.|+|++|+++|++++.
T Consensus 13 ~G~eITae~I~~IL~AAG-veVd~~~~~ala~aL~gkdIeElIa~~~~ 59 (106)
T cd05832 13 AGKEINEENLKKVLEAAG-IEVDEARVKALVAALEEVNIDEAIKKAAV 59 (106)
T ss_pred cCCCCCHHHHHHHHHHhC-CcccHHHHHHHHHHHcCCCHHHHHHhccc
Confidence 466999999999999999 99999999999999999999999998765
No 12
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=99.44 E-value=1.4e-13 Score=95.61 Aligned_cols=47 Identities=9% Similarity=0.086 Sum_probs=43.7
Q ss_pred ccccCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhhcCC
Q 044925 9 VQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLNVGS 56 (103)
Q Consensus 9 ~~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~v~a 56 (103)
-++.+|.++|++||+++| |+++..+++.|++.|+|++|+++|.++.+
T Consensus 13 ~g~~iT~e~I~~IL~AAG-v~ve~~~~~~la~~L~gk~i~eli~~~~~ 59 (105)
T TIGR03685 13 AGKEINEENLKAVLEAAG-VEVDEARVKALVAALEGVNIEEAIKKAAA 59 (105)
T ss_pred cCCCCCHHHHHHHHHHhC-CcccHHHHHHHHHHHcCCCHHHHHHhhhc
Confidence 356999999999999999 99999999999999999999999987763
No 13
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=98.56 E-value=4.5e-08 Score=78.53 Aligned_cols=18 Identities=56% Similarity=0.973 Sum_probs=15.4
Q ss_pred hcccccccccCCCCCCCC
Q 044925 86 KEETKEESDDDMGLSLFD 103 (103)
Q Consensus 86 keeeeEE~ddDmGFgLFD 103 (103)
++||+|||||||||||||
T Consensus 293 ~~~~~ee~~~~~g~~lf~ 310 (310)
T PTZ00135 293 PAEEEEEEEDDMGFGLFD 310 (310)
T ss_pred ccccccCcchhccccCCC
Confidence 356778889999999998
No 14
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=97.87 E-value=5.4e-06 Score=67.21 Aligned_cols=17 Identities=53% Similarity=0.986 Sum_probs=12.8
Q ss_pred hcccccccccCCCCC-CC
Q 044925 86 KEETKEESDDDMGLS-LF 102 (103)
Q Consensus 86 keeeeEE~ddDmGFg-LF 102 (103)
++|++||+||||||| ||
T Consensus 306 ~~~~~e~~~~d~~~~~~~ 323 (323)
T PTZ00240 306 KEEEEESDEDDFGMGALF 323 (323)
T ss_pred ccCCccCcccccCccccC
Confidence 356677888999997 55
No 15
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=97.19 E-value=0.00027 Score=49.14 Aligned_cols=45 Identities=9% Similarity=-0.063 Sum_probs=27.5
Q ss_pred eecccccCCchhhHhhhhh-cccccccHHHHHHHHHHhcCCChHHHhhhcCCCCccc
Q 044925 6 MDTVQIFWPHNTIDSGLVE-FSFFTSQPEKIATLIKLFEKRSADELYLNVGSGGAHL 61 (103)
Q Consensus 6 ~~~~~~~~~~~~i~~~l~~-~g~vevdaekI~~li~aL~gk~I~eLIa~v~agg~a~ 61 (103)
+..++.+|+...++.++++ -| . +|..||.....| +.++++||+++
T Consensus 26 L~aaGveVe~~~~~~~~~aLaG-k-----~V~eli~~g~~k-----l~~~~~~~~a~ 71 (105)
T cd04411 26 LSAAGAEIEPERVKLFLSALNG-K-----NIDEVISKGKEL-----MSSQAAAAAAP 71 (105)
T ss_pred HHHcCCCcCHHHHHHHHHHHcC-C-----CHHHHHHHHHhh-----ccCCCCccccc
Confidence 4567888888888888888 45 3 355566544322 34455444443
No 16
>COG2058 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]
Probab=97.15 E-value=0.00029 Score=49.65 Aligned_cols=26 Identities=4% Similarity=-0.038 Sum_probs=20.3
Q ss_pred hhhhcccccccHHHHHHHHHHhcCCChH
Q 044925 21 GLVEFSFFTSQPEKIATLIKLFEKRSAD 48 (103)
Q Consensus 21 ~l~~~g~vevdaekI~~li~aL~gk~I~ 48 (103)
.|-.+| =+||+++|.+|++.. |.+|+
T Consensus 9 lL~~ag-kei~e~~l~~vl~aa-Gveve 34 (109)
T COG2058 9 LLHLAG-KEITEDNLKSVLEAA-GVEVE 34 (109)
T ss_pred HHHHcc-CcCCHHHHHHHHHHc-CCCcc
Confidence 466778 699999999999965 55554
No 17
>PRK06402 rpl12p 50S ribosomal protein L12P; Reviewed
Probab=97.11 E-value=0.00071 Score=47.32 Aligned_cols=27 Identities=11% Similarity=0.060 Sum_probs=21.7
Q ss_pred hhhhcccccccHHHHHHHHHHhcCCChHH
Q 044925 21 GLVEFSFFTSQPEKIATLIKLFEKRSADE 49 (103)
Q Consensus 21 ~l~~~g~vevdaekI~~li~aL~gk~I~e 49 (103)
+|...| .+||+++|++|+++. |.++++
T Consensus 9 LL~~~g-~~it~e~I~~IL~AA-GveVee 35 (106)
T PRK06402 9 LLHSAG-KEINEDNLKKVLEAA-GVEVDE 35 (106)
T ss_pred HHHhcC-CCCCHHHHHHHHHHc-CCCccH
Confidence 567778 799999999999976 566654
No 18
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=96.89 E-value=0.00072 Score=47.80 Aligned_cols=38 Identities=18% Similarity=0.205 Sum_probs=27.7
Q ss_pred eeecccccCCchhhHhhhhhcccccccHHHHHHHHH----HhcCCCh
Q 044925 5 YMDTVQIFWPHNTIDSGLVEFSFFTSQPEKIATLIK----LFEKRSA 47 (103)
Q Consensus 5 ~~~~~~~~~~~~~i~~~l~~~g~vevdaekI~~li~----aL~gk~I 47 (103)
.+++|+.+++.+.|+.+|+++- .-+|..||. .|...+.
T Consensus 26 Il~sVG~E~d~e~i~~visel~-----GK~i~ElIA~G~eklAsvps 67 (112)
T KOG3449|consen 26 ILESVGAEIDDERINLVLSELK-----GKDIEELIAAGREKLASVPS 67 (112)
T ss_pred HHHHhCcccCHHHHHHHHHHhc-----CCCHHHHHHHhHHHHhcCCC
Confidence 3678999999999999999987 234555555 5544443
No 19
>cd05831 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and
Probab=96.65 E-value=0.0035 Score=43.34 Aligned_cols=27 Identities=15% Similarity=0.124 Sum_probs=21.8
Q ss_pred hhhhcccccccHHHHHHHHHHhcCCChHH
Q 044925 21 GLVEFSFFTSQPEKIATLIKLFEKRSADE 49 (103)
Q Consensus 21 ~l~~~g~vevdaekI~~li~aL~gk~I~e 49 (103)
+|...| .+||+++|++|+++. |.+++.
T Consensus 10 iL~d~~-~~~Tae~I~~ilkAa-Gveve~ 36 (103)
T cd05831 10 ILHDDG-IEITADNINALLKAA-GVNVEP 36 (103)
T ss_pred HHccCC-CCCCHHHHHHHHHHc-CCcccH
Confidence 677788 999999999999976 455553
No 20
>PRK04019 rplP0 acidic ribosomal protein P0; Validated
Probab=96.55 E-value=0.003 Score=50.94 Aligned_cols=38 Identities=18% Similarity=0.072 Sum_probs=27.7
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHhcC-CChHHHhhhcC
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEK-RSADELYLNVG 55 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL~g-k~I~eLIa~v~ 55 (103)
++|+++++.+|..+ .-++..|...|.+ .+|.+-|.+..
T Consensus 254 ~~t~e~~~~il~kA------~~~~~ala~~~~~~~~~~~~~~~~~ 292 (330)
T PRK04019 254 IVTPETADDILSKA------VAQALALAAALADKDALDEELKEVL 292 (330)
T ss_pred CCChhhHHHHHHHH------HHHHHHHHHHhcCcccccHHHHhhc
Confidence 46677777777666 3566677778988 99999997654
No 21
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=96.41 E-value=0.002 Score=44.79 Aligned_cols=26 Identities=12% Similarity=0.034 Sum_probs=20.3
Q ss_pred hhhhcccccccHHHHHHHHHHhcCCChH
Q 044925 21 GLVEFSFFTSQPEKIATLIKLFEKRSAD 48 (103)
Q Consensus 21 ~l~~~g~vevdaekI~~li~aL~gk~I~ 48 (103)
+|.-.| .+||.++|++||+.- |.+++
T Consensus 9 ll~~~g-~~iT~e~I~~IL~AA-Gv~ve 34 (105)
T TIGR03685 9 LLHSAG-KEINEENLKAVLEAA-GVEVD 34 (105)
T ss_pred HHHhcC-CCCCHHHHHHHHHHh-CCccc
Confidence 566678 799999999999975 44444
No 22
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=96.11 E-value=0.0085 Score=41.92 Aligned_cols=26 Identities=12% Similarity=-0.014 Sum_probs=20.3
Q ss_pred hhhhcccccccHHHHHHHHHHhcCCChH
Q 044925 21 GLVEFSFFTSQPEKIATLIKLFEKRSAD 48 (103)
Q Consensus 21 ~l~~~g~vevdaekI~~li~aL~gk~I~ 48 (103)
+|...| .+||+++|++||+.- |.+++
T Consensus 9 LL~~~G-~eITae~I~~IL~AA-GveVd 34 (106)
T cd05832 9 LLHYAG-KEINEENLKKVLEAA-GIEVD 34 (106)
T ss_pred HHHhcC-CCCCHHHHHHHHHHh-CCccc
Confidence 567778 799999999999965 44444
No 23
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=94.79 E-value=0.023 Score=39.76 Aligned_cols=13 Identities=0% Similarity=0.210 Sum_probs=7.1
Q ss_pred cccHHHHHHHHHH
Q 044925 29 TSQPEKIATLIKL 41 (103)
Q Consensus 29 evdaekI~~li~a 41 (103)
++|+++|++||++
T Consensus 17 ~pTa~dI~~IL~A 29 (109)
T cd05833 17 SPSAADVKKILGS 29 (109)
T ss_pred CCCHHHHHHHHHH
Confidence 4555555555554
No 24
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=91.14 E-value=0.12 Score=36.38 Aligned_cols=19 Identities=16% Similarity=0.270 Sum_probs=14.2
Q ss_pred cccHHHHHHHHHHhcCCChH
Q 044925 29 TSQPEKIATLIKLFEKRSAD 48 (103)
Q Consensus 29 evdaekI~~li~aL~gk~I~ 48 (103)
++++++|++|++.. |.+++
T Consensus 17 ~pta~dI~~IL~Aa-Gvevd 35 (113)
T PLN00138 17 CPSAEDLKDILGSV-GADAD 35 (113)
T ss_pred CCCHHHHHHHHHHc-CCccc
Confidence 68999999999965 34454
No 25
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=89.86 E-value=0.24 Score=34.98 Aligned_cols=14 Identities=0% Similarity=0.228 Sum_probs=9.6
Q ss_pred cccHHHHHHHHHHh
Q 044925 29 TSQPEKIATLIKLF 42 (103)
Q Consensus 29 evdaekI~~li~aL 42 (103)
.+++++|++||+..
T Consensus 19 ~pTaddI~kIL~Aa 32 (112)
T PTZ00373 19 NPTKKEVKNVLSAV 32 (112)
T ss_pred CCCHHHHHHHHHHc
Confidence 47777777777754
No 26
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=84.47 E-value=0.58 Score=38.25 Aligned_cols=12 Identities=8% Similarity=0.243 Sum_probs=5.4
Q ss_pred cccHHHHHHHHH
Q 044925 29 TSQPEKIATLIK 40 (103)
Q Consensus 29 evdaekI~~li~ 40 (103)
-+|.+.+.-+|.
T Consensus 238 ~pt~~si~~~i~ 249 (323)
T PTZ00240 238 IPTAATIGPMLV 249 (323)
T ss_pred CCcHHHHHHHHH
Confidence 345555544333
No 27
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=71.44 E-value=4.8 Score=23.11 Aligned_cols=30 Identities=13% Similarity=0.246 Sum_probs=27.0
Q ss_pred cCCchhhHhhhhhccccc-ccHHHHHHHHHHh
Q 044925 12 FWPHNTIDSGLVEFSFFT-SQPEKIATLIKLF 42 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~ve-vdaekI~~li~aL 42 (103)
.|+.+++.++|..+| +. ++.+.+..++..+
T Consensus 4 ~i~~~~~~~~l~~~g-~~~~s~~e~~~l~~~~ 34 (54)
T PF13833_consen 4 KITREEFRRALSKLG-IKDLSEEEVDRLFREF 34 (54)
T ss_dssp EEEHHHHHHHHHHTT-SSSSCHHHHHHHHHHH
T ss_pred EECHHHHHHHHHHhC-CCCCCHHHHHHHHHhc
Confidence 578899999998889 99 9999999999966
No 28
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=68.67 E-value=4.5 Score=24.90 Aligned_cols=39 Identities=15% Similarity=0.244 Sum_probs=33.0
Q ss_pred CCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhh
Q 044925 13 WPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYL 52 (103)
Q Consensus 13 ~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa 52 (103)
||.+=+.-.|...| ++.+.-+|..||+...-|=|.+++.
T Consensus 3 IPD~v~~~yL~~~G-~~~~D~rv~RLvSLaaQKFisdI~~ 41 (51)
T PF03540_consen 3 IPDEVTDYYLERSG-FQTSDPRVKRLVSLAAQKFISDIAN 41 (51)
T ss_pred CCHHHHHHHHHHCC-CCCCCHhHHHHHHHHHHHHHHHHHH
Confidence 56667888999999 9999999999999887777777764
No 29
>KOG0031 consensus Myosin regulatory light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=68.48 E-value=10 Score=28.64 Aligned_cols=41 Identities=15% Similarity=0.266 Sum_probs=34.6
Q ss_pred ccCCchhhHhhhhhcccccccHHHHHHHHH-----------------HhcCCChHHHhh
Q 044925 11 IFWPHNTIDSGLVEFSFFTSQPEKIATLIK-----------------LFEKRSADELYL 52 (103)
Q Consensus 11 ~~~~~~~i~~~l~~~g~vevdaekI~~li~-----------------aL~gk~I~eLIa 52 (103)
-+|..+||+..|.++| =.++.+.|+..++ -|.|-+.++.|-
T Consensus 47 G~IdkeDL~d~~aSlG-k~~~d~elDaM~~Ea~gPINft~FLTmfGekL~gtdpe~~I~ 104 (171)
T KOG0031|consen 47 GFIDKEDLRDMLASLG-KIASDEELDAMMKEAPGPINFTVFLTMFGEKLNGTDPEEVIL 104 (171)
T ss_pred CcccHHHHHHHHHHcC-CCCCHHHHHHHHHhCCCCeeHHHHHHHHHHHhcCCCHHHHHH
Confidence 3789999999999999 5599999999998 667777777774
No 30
>KOG1762 consensus 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis]
Probab=68.16 E-value=3.1 Score=29.58 Aligned_cols=20 Identities=10% Similarity=-0.017 Sum_probs=11.6
Q ss_pred cccCCchhhHhhhhhcccccc
Q 044925 10 QIFWPHNTIDSGLVEFSFFTS 30 (103)
Q Consensus 10 ~~~~~~~~i~~~l~~~g~vev 30 (103)
++.|+.+.|-.+++++| +++
T Consensus 20 ~i~it~dki~tl~kaa~-v~v 39 (114)
T KOG1762|consen 20 EIEVTADKINTLTKAAG-VNV 39 (114)
T ss_pred ceeeehhhhhhHHHhcc-Ccc
Confidence 45566666666666666 533
No 31
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=64.05 E-value=9.7 Score=25.72 Aligned_cols=36 Identities=0% Similarity=0.075 Sum_probs=33.3
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChH
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSAD 48 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~ 48 (103)
-+|.+++-+.=+..| |.++..+...+++.|+|++|.
T Consensus 14 ~iT~~eLlkyskqy~-i~it~~QA~~I~~~lr~k~in 49 (85)
T PF11116_consen 14 NITAKELLKYSKQYN-ISITKKQAEQIANILRGKNIN 49 (85)
T ss_pred cCCHHHHHHHHHHhC-CCCCHHHHHHHHHHHhcCCCC
Confidence 468899999999999 999999999999999999885
No 32
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=63.46 E-value=9.6 Score=26.04 Aligned_cols=32 Identities=19% Similarity=0.130 Sum_probs=18.9
Q ss_pred CCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHH
Q 044925 13 WPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADE 49 (103)
Q Consensus 13 ~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~e 49 (103)
||.++|..+|+.++ .+.+..+++++-.+|..+
T Consensus 1 It~e~V~~~lG~v~-----~~~i~~l~~ai~~~d~~~ 32 (143)
T PF12169_consen 1 ITAEDVREILGLVD-----EEQIFELLDAILEGDAAE 32 (143)
T ss_dssp B-HHHHHHHHTHTS-----THHHHHHHHHHHTT-HHH
T ss_pred CCHHHHHHHHCCCC-----HHHHHHHHHHHHcCCHHH
Confidence 57788888888877 455666666433333333
No 33
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=51.12 E-value=11 Score=21.02 Aligned_cols=29 Identities=21% Similarity=0.327 Sum_probs=20.9
Q ss_pred cCCchhhHhhhhhcccccccHHH--HHHHHHH
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEK--IATLIKL 41 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaek--I~~li~a 41 (103)
-|+.++|++-|.+.| |.+.... -+.|++.
T Consensus 3 tWs~~~L~~wL~~~g-i~~~~~~~~rd~Ll~~ 33 (38)
T PF10281_consen 3 TWSDSDLKSWLKSHG-IPVPKSAKTRDELLKL 33 (38)
T ss_pred CCCHHHHHHHHHHcC-CCCCCCCCCHHHHHHH
Confidence 489999999999999 7665432 4444443
No 34
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=49.10 E-value=18 Score=23.29 Aligned_cols=36 Identities=19% Similarity=0.331 Sum_probs=22.9
Q ss_pred cccCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChH
Q 044925 10 QIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSAD 48 (103)
Q Consensus 10 ~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~ 48 (103)
+.++|.++|...|.... ++.++|..|+..|....|.
T Consensus 19 ~G~lT~~eI~~~L~~~~---~~~e~id~i~~~L~~~gI~ 54 (82)
T PF03979_consen 19 KGYLTYDEINDALPEDD---LDPEQIDEIYDTLEDEGIE 54 (82)
T ss_dssp HSS-BHHHHHHH-S-S------HHHHHHHHHHHHTT---
T ss_pred cCcCCHHHHHHHcCccC---CCHHHHHHHHHHHHHCCCE
Confidence 45789999999998554 7889999999999777665
No 35
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=45.30 E-value=23 Score=22.59 Aligned_cols=28 Identities=4% Similarity=0.057 Sum_probs=25.4
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHH
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIK 40 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~ 40 (103)
.++.+++-.++...| ++++.+.|.++++
T Consensus 13 ~l~d~~m~~if~l~~-~~vs~~el~a~lr 40 (68)
T PF07308_consen 13 DLKDDDMIEIFALAG-FEVSKAELSAWLR 40 (68)
T ss_pred cCChHHHHHHHHHcC-CccCHHHHHHHHC
Confidence 467889999999999 9999999999887
No 36
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=44.79 E-value=58 Score=18.83 Aligned_cols=34 Identities=9% Similarity=0.112 Sum_probs=23.9
Q ss_pred hhhHhhhhhcccccccHHHHHHHHHHh---cCCChHHHhh
Q 044925 16 NTIDSGLVEFSFFTSQPEKIATLIKLF---EKRSADELYL 52 (103)
Q Consensus 16 ~~i~~~l~~~g~vevdaekI~~li~aL---~gk~I~eLIa 52 (103)
+++...|.++| .+...+..+++.+ .+.++.++|.
T Consensus 4 ~d~~~AL~~LG---y~~~e~~~av~~~~~~~~~~~e~~ik 40 (47)
T PF07499_consen 4 EDALEALISLG---YSKAEAQKAVSKLLEKPGMDVEELIK 40 (47)
T ss_dssp HHHHHHHHHTT---S-HHHHHHHHHHHHHSTTS-HHHHHH
T ss_pred HHHHHHHHHcC---CCHHHHHHHHHHhhcCCCCCHHHHHH
Confidence 67888999999 4566667666655 6778888885
No 37
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=39.03 E-value=14 Score=22.98 Aligned_cols=18 Identities=17% Similarity=-0.007 Sum_probs=8.9
Q ss_pred ccccCCchhhHhhhhhcc
Q 044925 9 VQIFWPHNTIDSGLVEFS 26 (103)
Q Consensus 9 ~~~~~~~~~i~~~l~~~g 26 (103)
+|..++.+++.++|..+|
T Consensus 15 lG~~i~~~~i~~~L~~lg 32 (70)
T PF03484_consen 15 LGIDISPEEIIKILKRLG 32 (70)
T ss_dssp HTS---HHHHHHHHHHTT
T ss_pred hCCCCCHHHHHHHHHHCC
Confidence 455556666666666666
No 38
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=38.15 E-value=52 Score=24.40 Aligned_cols=41 Identities=15% Similarity=0.181 Sum_probs=33.2
Q ss_pred ccCCchhhHhhhhhcccccccHHHHHHHHHHhc----CCChHHHhh
Q 044925 11 IFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFE----KRSADELYL 52 (103)
Q Consensus 11 ~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~----gk~I~eLIa 52 (103)
-.|+.+++.++|+++| ..++..-|+.++..+. ..+..++|.
T Consensus 35 G~I~~~el~~ilr~lg-~~~s~~ei~~l~~~~d~~~~~idf~~Fl~ 79 (160)
T COG5126 35 GLIDRNELGKILRSLG-FNPSEAEINKLFEEIDAGNETVDFPEFLT 79 (160)
T ss_pred CCCcHHHHHHHHHHcC-CCCcHHHHHHHHHhccCCCCccCHHHHHH
Confidence 3588999999999999 8888888999999775 355567765
No 39
>PF05788 Orbi_VP1: Orbivirus RNA-dependent RNA polymerase (VP1); InterPro: IPR008723 This family consists of the RNA-dependent RNA polymerase protein VP1 from the Orbivirus. VP1 may have both enzymatic and structural roles in the virus life cycle [].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=38.11 E-value=16 Score=34.85 Aligned_cols=41 Identities=32% Similarity=0.510 Sum_probs=35.3
Q ss_pred Cceeeeecc----------cccCCchhhHhhhhhcccccccHHHHHHHHHHh
Q 044925 1 MRVQYMDTV----------QIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLF 42 (103)
Q Consensus 1 ~~~~~~~~~----------~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL 42 (103)
+|+.|||.+ .-+||.|.|-++|..+| +.-+++.+..++..|
T Consensus 1116 ~r~SYvDrID~ILR~DvVMRGfiTsn~Il~vle~iG-~~h~a~Dl~~iF~lm 1166 (1301)
T PF05788_consen 1116 MRMSYVDRIDSILRGDVVMRGFITSNTILNVLEKIG-FGHSASDLATIFTLM 1166 (1301)
T ss_pred hHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHhc-CCCCHHHHHHHHHHh
Confidence 467787754 34899999999999999 999999999999966
No 40
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=35.21 E-value=23 Score=21.58 Aligned_cols=15 Identities=20% Similarity=0.394 Sum_probs=7.8
Q ss_pred ccccHHHHHHHHHHh
Q 044925 28 FTSQPEKIATLIKLF 42 (103)
Q Consensus 28 vevdaekI~~li~aL 42 (103)
++++.+.+..+++.|
T Consensus 17 ~~i~~~ei~~~L~~l 31 (71)
T smart00874 17 LDLSAEEIEEILKRL 31 (71)
T ss_pred CCCCHHHHHHHHHHC
Confidence 455555555555544
No 41
>PHA02770 hypothetical protein; Provisional
Probab=34.55 E-value=30 Score=22.75 Aligned_cols=19 Identities=21% Similarity=0.468 Sum_probs=17.3
Q ss_pred HHHHHHHHhcCCChHHHhh
Q 044925 34 KIATLIKLFEKRSADELYL 52 (103)
Q Consensus 34 kI~~li~aL~gk~I~eLIa 52 (103)
+|+.+|+.|..|+|+++|.
T Consensus 3 qieeiik~lnkkdikdiit 21 (81)
T PHA02770 3 QIEEIIKTLNKKDIKDIIT 21 (81)
T ss_pred HHHHHHHHhhhhhHHHHHh
Confidence 6888999999999999995
No 42
>PF10815 ComZ: ComZ; InterPro: IPR024558 ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon [].
Probab=32.85 E-value=22 Score=22.38 Aligned_cols=37 Identities=16% Similarity=0.329 Sum_probs=30.2
Q ss_pred eeeeecccccCCchhhHhhhhhcccccccHHHHHHHHHHh
Q 044925 3 VQYMDTVQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLF 42 (103)
Q Consensus 3 ~~~~~~~~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL 42 (103)
.+||+.--|.+|+ -+..|...| |+.+.+.|+-++..|
T Consensus 4 m~FmqIaMK~lPE--ak~~L~k~G-IeLsme~~qP~m~L~ 40 (56)
T PF10815_consen 4 MEFMQIAMKYLPE--AKEELDKKG-IELSMEMLQPLMQLL 40 (56)
T ss_pred hHHHHHHHHHhHH--HHHHHHHcC-ccCCHHHHHHHHHHH
Confidence 3566666677777 689999999 999999999888855
No 43
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=32.82 E-value=73 Score=16.87 Aligned_cols=30 Identities=13% Similarity=0.172 Sum_probs=27.0
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHh
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLF 42 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL 42 (103)
.++.+++..++...| ...+.+.+..+++.+
T Consensus 16 ~l~~~e~~~~l~~~~-~~~~~~~~~~~~~~~ 45 (63)
T cd00051 16 TISADELKAALKSLG-EGLSEEEIDEMIREV 45 (63)
T ss_pred cCcHHHHHHHHHHhC-CCCCHHHHHHHHHHh
Confidence 578899999999999 999999999998877
No 44
>cd05031 S-100A10_like S-100A10_like: S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1_like group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions.
Probab=32.39 E-value=50 Score=21.18 Aligned_cols=31 Identities=6% Similarity=0.128 Sum_probs=26.9
Q ss_pred ccCCchhhHhhhhh-----cccccccHHHHHHHHHHh
Q 044925 11 IFWPHNTIDSGLVE-----FSFFTSQPEKIATLIKLF 42 (103)
Q Consensus 11 ~~~~~~~i~~~l~~-----~g~vevdaekI~~li~aL 42 (103)
-.|+.+++.++|.+ +| ..++.+.|+.+++.+
T Consensus 25 G~Is~~El~~~l~~~~g~~lg-~~~s~~ei~~~~~~~ 60 (94)
T cd05031 25 NTLSRKELKKLMEKELSEFLK-NQKDPMAVDKIMKDL 60 (94)
T ss_pred CeECHHHHHHHHHHHhHHHhh-ccccHHHHHHHHHHh
Confidence 47999999999987 67 778888999999877
No 45
>smart00523 DWA Domain A in dwarfin family proteins.
Probab=32.11 E-value=35 Score=23.81 Aligned_cols=26 Identities=31% Similarity=0.459 Sum_probs=21.2
Q ss_pred HHHHHHHHhcCCChHHHhhhcCCCCc
Q 044925 34 KIATLIKLFEKRSADELYLNVGSGGA 59 (103)
Q Consensus 34 kI~~li~aL~gk~I~eLIa~v~agg~ 59 (103)
.+.+|++.|+.+.+++|+..+.+-|.
T Consensus 9 ~~~sL~KklK~k~le~L~~AV~s~g~ 34 (109)
T smart00523 9 ATESLLKKLKKKQLEELLQAVESKGG 34 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 46788999999999999998876553
No 46
>PF03575 Peptidase_S51: Peptidase family S51; InterPro: IPR005320 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S51 (clan PC(S)). The type example being dipeptidase E (alpha-aspartyl dipeptidase) from Escherichia coli. The family contains alpha-aspartyl dipeptidases (dipeptidase E) and cyanophycinases. The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E has been determine at 1.2-A resolution. The structure of this 25kDa enzyme consists of two mixed beta-sheets forming a V, flanked by six alpha-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organisation of the catalytic triad differ from those of the known serine proteases. This enzyme appears to represent a new example of convergent evolution of peptidase activity []. Alpha-aspartyl dipeptidase hydrolyses dipeptides containing N-terminal aspartate residues, asp-|-xaa. It does not act on peptides with N-terminal Glu, Asn or Gln, nor does it cleave isoaspartyl peptides. In the cyanobacteria, cyanophycinase is an exopeptidase that catalyses the hydrolytic cleavage of multi-l-arginyl-poly-l-aspartic acid (cyanophycin; a water- insoluble reserve polymer) into aspartate-arginine dipeptides.; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis; PDB: 3EN0_B 1FYE_A 1FY2_A 3L4E_A.
Probab=32.05 E-value=31 Score=24.18 Aligned_cols=50 Identities=14% Similarity=0.096 Sum_probs=37.6
Q ss_pred ceeeeecccccCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhh
Q 044925 2 RVQYMDTVQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLN 53 (103)
Q Consensus 2 ~~~~~~~~~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~ 53 (103)
+|++++.... +..++.+.|..+.+|-+..-+=..+++.|++..+.++|..
T Consensus 15 ~v~~l~~~~~--~~~~~~~~i~~ad~I~~~GG~~~~l~~~l~~t~l~~~i~~ 64 (154)
T PF03575_consen 15 EVDQLDLSDR--NDADILEAIREADAIFLGGGDTFRLLRQLKETGLDEAIRE 64 (154)
T ss_dssp EEEECCCTSC--GHHHHHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHH
T ss_pred EEEEEeccCC--ChHHHHHHHHhCCEEEECCCCHHHHHHHHHhCCHHHHHHH
Confidence 4666666655 4557888888888799999999999999999999999975
No 47
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=32.05 E-value=60 Score=21.08 Aligned_cols=40 Identities=5% Similarity=0.108 Sum_probs=31.7
Q ss_pred cCCchhhHhhhhh-----cccccccHHHHHHHHHHhc-----CCChHHHhh
Q 044925 12 FWPHNTIDSGLVE-----FSFFTSQPEKIATLIKLFE-----KRSADELYL 52 (103)
Q Consensus 12 ~~~~~~i~~~l~~-----~g~vevdaekI~~li~aL~-----gk~I~eLIa 52 (103)
.++.++++++|.+ +| -..+.+.++.+++.+. ..+..+.+.
T Consensus 26 ~I~~~eL~~ll~~~~~~~lg-~~~~~~~v~~~i~~~D~n~dG~v~f~eF~~ 75 (88)
T cd05027 26 KLKKSELKELINNELSHFLE-EIKEQEVVDKVMETLDSDGDGECDFQEFMA 75 (88)
T ss_pred EECHHHHHHHHHHHhHHHhc-CCCCHHHHHHHHHHhCCCCCCcCcHHHHHH
Confidence 5999999999999 99 7788888999999772 134555553
No 48
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.76 E-value=69 Score=22.77 Aligned_cols=29 Identities=10% Similarity=0.165 Sum_probs=25.4
Q ss_pred CCchhhHhhhhhcccccccHHHHHHHHHHh
Q 044925 13 WPHNTIDSGLVEFSFFTSQPEKIATLIKLF 42 (103)
Q Consensus 13 ~~~~~i~~~l~~~g~vevdaekI~~li~aL 42 (103)
-|..+|++||..-+ +.++.|.+++++.-+
T Consensus 80 ~t~~ElRsIla~e~-~~~s~E~l~~Ildiv 108 (114)
T COG1460 80 RTPDELRSILAKER-VMLSDEELDKILDIV 108 (114)
T ss_pred CCHHHHHHHHHHcc-CCCCHHHHHHHHHHH
Confidence 47789999999999 999999999988754
No 49
>PRK00994 F420-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional
Probab=26.14 E-value=33 Score=27.74 Aligned_cols=46 Identities=15% Similarity=0.196 Sum_probs=38.8
Q ss_pred ceeeeecccccCCchhhHhhhhhcccccccHHHHHHHHHHh-cCCCh
Q 044925 2 RVQYMDTVQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLF-EKRSA 47 (103)
Q Consensus 2 ~~~~~~~~~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL-~gk~I 47 (103)
|-+|+|.++--.=-.|+-+||..-|.+-.-.+-|+++|... +|+.+
T Consensus 124 rREFLDP~EMa~fNaD~~kVLa~tG~~RlvQ~elD~vi~~v~~G~e~ 170 (277)
T PRK00994 124 RREFLDPVEMALFNADVLKVLAGTGAVRLVQEELDKVIDQVKEGKEI 170 (277)
T ss_pred hhhccCHHHHHHhhhhHHHHHHhhhHHHHHHHHHHHHHHHHhcCCCc
Confidence 66888888887778899999999998888888899999977 56644
No 50
>PRK06770 hypothetical protein; Provisional
Probab=25.93 E-value=65 Score=24.57 Aligned_cols=25 Identities=16% Similarity=0.304 Sum_probs=20.4
Q ss_pred hcccccccHHHHHHHHHHhcCCChH
Q 044925 24 EFSFFTSQPEKIATLIKLFEKRSAD 48 (103)
Q Consensus 24 ~~g~vevdaekI~~li~aL~gk~I~ 48 (103)
-.||++++.++|++|.+.|..-+..
T Consensus 89 KwG~~~mT~enI~~l~~~i~~sn~~ 113 (180)
T PRK06770 89 KWGFIEMTQENIEKLKDIINSSNFV 113 (180)
T ss_pred ccceEecCHHHHHHHHHHHhccchh
Confidence 4699999999999999988755553
No 51
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=25.76 E-value=59 Score=18.47 Aligned_cols=22 Identities=9% Similarity=0.170 Sum_probs=18.3
Q ss_pred eeecccccCCchhhHhhhhhcc
Q 044925 5 YMDTVQIFWPHNTIDSGLVEFS 26 (103)
Q Consensus 5 ~~~~~~~~~~~~~i~~~l~~~g 26 (103)
|+..+-..+++.+|++.++.+|
T Consensus 2 ~v~nlp~~~t~~~l~~~f~~~g 23 (70)
T PF00076_consen 2 YVGNLPPDVTEEELRDFFSQFG 23 (70)
T ss_dssp EEESETTTSSHHHHHHHHHTTS
T ss_pred EEcCCCCcCCHHHHHHHHHHhh
Confidence 6667778888999999988888
No 52
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=25.72 E-value=56 Score=21.63 Aligned_cols=25 Identities=8% Similarity=0.145 Sum_probs=17.7
Q ss_pred ceeeeecccccCCchhhHhhhhhcc
Q 044925 2 RVQYMDTVQIFWPHNTIDSGLVEFS 26 (103)
Q Consensus 2 ~~~~~~~~~~~~~~~~i~~~l~~~g 26 (103)
.+++.|..+..+|.+.|..+|..+|
T Consensus 22 ~~~~~d~~k~p~s~~el~~~l~~~~ 46 (110)
T PF03960_consen 22 EYEFIDYKKEPLSREELRELLSKLG 46 (110)
T ss_dssp -EEEEETTTS---HHHHHHHHHHHT
T ss_pred CeEeehhhhCCCCHHHHHHHHHHhc
Confidence 4677888888888888888888888
No 53
>PTZ00135 60S acidic ribosomal protein P0; Provisional
Probab=25.14 E-value=36 Score=27.54 Aligned_cols=17 Identities=18% Similarity=0.094 Sum_probs=9.1
Q ss_pred hhhcccccccccCCCCC
Q 044925 84 EKKEETKEESDDDMGLS 100 (103)
Q Consensus 84 e~keeeeEE~ddDmGFg 100 (103)
++++||+|++..-..|+
T Consensus 294 ~~~~ee~~~~~g~~lf~ 310 (310)
T PTZ00135 294 AEEEEEEEDDMGFGLFD 310 (310)
T ss_pred cccccCcchhccccCCC
Confidence 44455666665544453
No 54
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=24.96 E-value=79 Score=21.38 Aligned_cols=23 Identities=17% Similarity=0.189 Sum_probs=19.8
Q ss_pred hhHhhhhhcccccccHHHHHHHHH
Q 044925 17 TIDSGLVEFSFFTSQPEKIATLIK 40 (103)
Q Consensus 17 ~i~~~l~~~g~vevdaekI~~li~ 40 (103)
-|...|...| +.+|.+.|+.+|.
T Consensus 76 ~v~~~L~~~g-i~~t~~~i~~~IE 98 (108)
T PF09682_consen 76 YVKERLKKKG-IKVTDEQIEGAIE 98 (108)
T ss_pred HHHHHHHHcC-CCCCHHHHHHHHH
Confidence 4667899999 7999999999887
No 55
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=24.78 E-value=1.2e+02 Score=23.02 Aligned_cols=37 Identities=14% Similarity=0.018 Sum_probs=27.3
Q ss_pred ccCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHh
Q 044925 11 IFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELY 51 (103)
Q Consensus 11 ~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLI 51 (103)
..||.++|+.++.... ..++|..+++++.++++...+
T Consensus 235 ~~It~~~v~~~~~~~~----~~~~i~~l~~ai~~~~~~~a~ 271 (337)
T PRK12402 235 GEITMEAAYEALGDVG----TDEVIESLLDAAEAGDFTDAR 271 (337)
T ss_pred CCCCHHHHHHHhCCCC----CHHHHHHHHHHHHcCCHHHHH
Confidence 4688888888765443 456888899988888887654
No 56
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=24.52 E-value=1.1e+02 Score=27.88 Aligned_cols=42 Identities=19% Similarity=0.429 Sum_probs=35.7
Q ss_pred chhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHhhhcCCCCcc
Q 044925 15 HNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELYLNVGSGGAH 60 (103)
Q Consensus 15 ~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLIa~v~agg~a 60 (103)
.+=+++.|...| . +.+.++ ++..|.-+++++|++.+|.|.-.
T Consensus 488 ~~lLe~~l~~~g-~--~~~~~~-~l~~~~~~~~edl~a~ig~g~~~ 529 (701)
T COG0317 488 RELLEKELSRLG-L--PKELEE-LLEKLNFKTVEDLYAAVGAGDIR 529 (701)
T ss_pred HHHHHHHHHHcC-C--ChHHHH-HHHHhCCCCHHHHHHHhccCCCC
Confidence 455788999999 4 889999 99999999999999999877643
No 57
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=24.41 E-value=31 Score=17.79 Aligned_cols=16 Identities=13% Similarity=0.094 Sum_probs=12.5
Q ss_pred ccCCchhhHhhhh-hcc
Q 044925 11 IFWPHNTIDSGLV-EFS 26 (103)
Q Consensus 11 ~~~~~~~i~~~l~-~~g 26 (103)
-+|+.+++.++|. ++|
T Consensus 15 G~I~~~el~~~l~~~lG 31 (31)
T PF13405_consen 15 GFIDFEELRAILRKSLG 31 (31)
T ss_dssp SEEEHHHHHHHHHHHTT
T ss_pred CcCcHHHHHHHHHHhcC
Confidence 3678888888888 776
No 58
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=24.39 E-value=97 Score=21.44 Aligned_cols=41 Identities=15% Similarity=0.082 Sum_probs=33.3
Q ss_pred ccCCchhhHhhhhhcccccccHHHHHHHHHHhcC-----CChHHHhh
Q 044925 11 IFWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEK-----RSADELYL 52 (103)
Q Consensus 11 ~~~~~~~i~~~l~~~g~vevdaekI~~li~aL~g-----k~I~eLIa 52 (103)
..++...+..++.++| ..++...|..+++.+.. .++.+++.
T Consensus 23 G~i~~~el~~~lr~lg-~~~t~~el~~~~~~~D~dg~g~I~~~eF~~ 68 (151)
T KOG0027|consen 23 GKISVEELGAVLRSLG-QNPTEEELRDLIKEIDLDGDGTIDFEEFLD 68 (151)
T ss_pred CcccHHHHHHHHHHcC-CCCCHHHHHHHHHHhCCCCCCeEcHHHHHH
Confidence 4688999999999999 89999999999997752 35555553
No 59
>PRK10853 putative reductase; Provisional
Probab=24.06 E-value=86 Score=21.55 Aligned_cols=25 Identities=8% Similarity=-0.037 Sum_probs=21.9
Q ss_pred ceeeeecccccCCchhhHhhhhhcc
Q 044925 2 RVQYMDTVQIFWPHNTIDSGLVEFS 26 (103)
Q Consensus 2 ~~~~~~~~~~~~~~~~i~~~l~~~g 26 (103)
.+++.|-.+..++.+.|+++|..+|
T Consensus 26 ~~~~~d~~k~p~s~~eL~~~l~~~g 50 (118)
T PRK10853 26 DYRFHDYRVDGLDSELLQGFIDELG 50 (118)
T ss_pred CcEEeehccCCcCHHHHHHHHHHcC
Confidence 3577888888999999999999999
No 60
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=23.59 E-value=1.1e+02 Score=17.78 Aligned_cols=38 Identities=16% Similarity=0.162 Sum_probs=19.8
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHhcCCChHHHh
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFEKRSADELY 51 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL~gk~I~eLI 51 (103)
.++...|.+++..=- -.++.+.|.++.++| |.++.+|+
T Consensus 21 gis~~tl~~~~~~~~-~~~~~~~l~~ia~~l-~~~~~el~ 58 (63)
T PF13443_consen 21 GISRSTLSRILNGKP-SNPSLDTLEKIAKAL-NCSPEELF 58 (63)
T ss_dssp T--HHHHHHHHTTT------HHHHHHHHHHH-T--HHHCT
T ss_pred CcCHHHHHHHHhccc-ccccHHHHHHHHHHc-CCCHHHHh
Confidence 345566666666321 257778888888877 66777776
No 61
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=23.53 E-value=1.2e+02 Score=18.91 Aligned_cols=30 Identities=17% Similarity=0.160 Sum_probs=22.3
Q ss_pred cCCchhhHhhhhhccccc-ccHHHHHHHHHHh
Q 044925 12 FWPHNTIDSGLVEFSFFT-SQPEKIATLIKLF 42 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~ve-vdaekI~~li~aL 42 (103)
.+|.+.|+++..+.| ++ +..+-...|-..+
T Consensus 2 ~~p~~~i~ria~~~G-i~ris~~a~~~l~~~~ 32 (65)
T smart00803 2 WLPKETIKDVAESLG-IGNLSDEAAKLLAEDV 32 (65)
T ss_pred CCCHHHHHHHHHHCC-CccccHHHHHHHHHHH
Confidence 478899999999999 76 6666555555544
No 62
>TIGR00135 gatC glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, C subunit. This model has been revised to remove the candidate sequence from Methanococcus jannaschii, now part of a related model.
Probab=22.17 E-value=99 Score=20.07 Aligned_cols=30 Identities=3% Similarity=-0.037 Sum_probs=23.0
Q ss_pred CCchhhHhhhhhcccccccHHHHHHHHHHhc
Q 044925 13 WPHNTIDSGLVEFSFFTSQPEKIATLIKLFE 43 (103)
Q Consensus 13 ~~~~~i~~~l~~~g~vevdaekI~~li~aL~ 43 (103)
+++++|+++-.-+- +.++.+.+..+.+.|.
T Consensus 1 i~~~~v~~lA~La~-L~l~eee~~~~~~~l~ 30 (93)
T TIGR00135 1 ISDEEVKHLAKLAR-LELSEEEAESFAGDLD 30 (93)
T ss_pred CCHHHHHHHHHHhC-CCCCHHHHHHHHHHHH
Confidence 46778888776666 8889888888888663
No 63
>PRK00034 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed
Probab=21.75 E-value=1e+02 Score=19.89 Aligned_cols=31 Identities=3% Similarity=-0.032 Sum_probs=25.5
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHhc
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFE 43 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL~ 43 (103)
.+++++|+++..-+- +.++.+.+..+.+.|+
T Consensus 2 ~i~~e~i~~la~La~-l~l~~ee~~~~~~~l~ 32 (95)
T PRK00034 2 AITREEVKHLAKLAR-LELSEEELEKFAGQLN 32 (95)
T ss_pred CCCHHHHHHHHHHhC-CCCCHHHHHHHHHHHH
Confidence 478899999888777 9999998888888653
No 64
>PF09504 RE_Bsp6I: Bsp6I restriction endonuclease; InterPro: IPR019037 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the restriction endonuclease Bsp6I, which recognises and cleaves the double-stranded sequence GC^NGC.
Probab=21.41 E-value=72 Score=24.32 Aligned_cols=32 Identities=6% Similarity=0.188 Sum_probs=24.0
Q ss_pred hhhhcccccccHHHHHHHHH---------------HhcCCChHHHhh
Q 044925 21 GLVEFSFFTSQPEKIATLIK---------------LFEKRSADELYL 52 (103)
Q Consensus 21 ~l~~~g~vevdaekI~~li~---------------aL~gk~I~eLIa 52 (103)
++..+|.|+||..+++.+++ --.|.|+.|.|+
T Consensus 2 ~~~~f~~ikidk~r~~~~~~~Y~~WK~LN~~IKn~~~RGiN~pd~fS 48 (180)
T PF09504_consen 2 AYKKFGYIKIDKARFEITIDAYFKWKDLNNYIKNIYSRGINFPDVFS 48 (180)
T ss_pred cccccCeEEecHHHHHHHHHHHHHHHHHHHHhhhccCCCccchHHHH
Confidence 35678889999999988887 226777777774
No 65
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=21.13 E-value=95 Score=23.01 Aligned_cols=31 Identities=13% Similarity=0.238 Sum_probs=27.8
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHhc
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLFE 43 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL~ 43 (103)
.|+.+.+..||+++| -..+.+.++.+|+.+.
T Consensus 108 ~Is~~eL~~vl~~lg-e~~~deev~~ll~~~d 138 (160)
T COG5126 108 YISIGELRRVLKSLG-ERLSDEEVEKLLKEYD 138 (160)
T ss_pred eecHHHHHHHHHhhc-ccCCHHHHHHHHHhcC
Confidence 578899999999999 9999999999999663
No 66
>COG1927 Mtd Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase [Energy production and conversion]
Probab=21.09 E-value=51 Score=26.40 Aligned_cols=46 Identities=20% Similarity=0.233 Sum_probs=37.5
Q ss_pred ceeeeecccccCCchhhHhhhhhcccccccHHHHHHHHHHh-cCCCh
Q 044925 2 RVQYMDTVQIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLF-EKRSA 47 (103)
Q Consensus 2 ~~~~~~~~~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL-~gk~I 47 (103)
|-.|+|.|+--.=..|+-++|.+-|.+-+-.+-|+++|... +|+.+
T Consensus 124 rREFLDPvEMA~fNaDv~kVLa~tGa~R~vQeaiD~~ie~vk~gk~~ 170 (277)
T COG1927 124 RREFLDPVEMASFNADVMKVLAATGAFRLVQEAIDKVIEDVKEGKEP 170 (277)
T ss_pred hhhhcCHHHHHhhhhHHHHHHHhccHHHHHHHHHHHHHHHHhcCCCc
Confidence 45677888777778899999999998889999999999966 45443
No 67
>PF09386 ParD: Antitoxin ParD; InterPro: IPR018985 ParD is a plasmid anti-toxin than forms a ribbon-helix-helix DNA binding structure []. It stabilises plasmids by inhibiting ParE toxicity in cells that express ParD and ParE. ParD forms a dimer and also regulates its own promoter (parDE). ; PDB: 2AN7_A.
Probab=21.08 E-value=93 Score=20.83 Aligned_cols=24 Identities=4% Similarity=0.169 Sum_probs=16.2
Q ss_pred ccccHHHHHHH--HHHhcCCChHHHh
Q 044925 28 FTSQPEKIATL--IKLFEKRSADELY 51 (103)
Q Consensus 28 vevdaekI~~l--i~aL~gk~I~eLI 51 (103)
|+++.++=..| +.+|+||.|+++.
T Consensus 6 IDiT~qQHQsLKAlAAlqGkTIKqYa 31 (79)
T PF09386_consen 6 IDITDQQHQSLKALAALQGKTIKQYA 31 (79)
T ss_dssp EEE-HHHHHHHHHHHHHHTS-HHHHH
T ss_pred eeCCHHHHHHHHHHHHHcCCcHHHHH
Confidence 66777665543 4599999999877
No 68
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=20.93 E-value=1.5e+02 Score=17.98 Aligned_cols=43 Identities=7% Similarity=-0.010 Sum_probs=26.4
Q ss_pred cccCCchhhHhhhhhcccccccHHHHHHHHHHh--cCCChHHHhh
Q 044925 10 QIFWPHNTIDSGLVEFSFFTSQPEKIATLIKLF--EKRSADELYL 52 (103)
Q Consensus 10 ~~~~~~~~i~~~l~~~g~vevdaekI~~li~aL--~gk~I~eLIa 52 (103)
++..+.+.+..++..+-.=+++..+|-+++.+| +|.+.+|+..
T Consensus 12 g~~Ls~~e~~~~~~~i~~g~~s~~qiaAfL~al~~kget~~Eiag 56 (66)
T PF02885_consen 12 GEDLSREEAKAAFDAILDGEVSDAQIAAFLMALRMKGETPEEIAG 56 (66)
T ss_dssp T----HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHH
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCcCHHHHHH
Confidence 456777888888777654478888899888865 7888888763
No 69
>PF04940 BLUF: Sensors of blue-light using FAD; InterPro: IPR007024 An FAD-binding domain, BLUF, exemplified by the N terminus of the AppA protein, (Q53119 from SWISSPROT), from Rhodobacter sphaeroides, is present in various proteins, primarily from Bacteria. The BLUF domain is involved in sensing blue-light (and possibly redox) using FAD and is similar to the flavin-binding PAS domains and cryptochromes. The predicted secondary structure reveals that the BLUF domain is a novel FAD-binding fold [].; PDB: 2IYG_A 2IYI_B 1X0P_A 2HFN_G 3MZI_A 2HFO_E 3GFZ_A 3GG1_B 2KB2_A 3GFY_A ....
Probab=20.90 E-value=70 Score=21.11 Aligned_cols=24 Identities=17% Similarity=0.106 Sum_probs=19.5
Q ss_pred ceeeeecccccCCchhhHhhhhhc
Q 044925 2 RVQYMDTVQIFWPHNTIDSGLVEF 25 (103)
Q Consensus 2 ~~~~~~~~~~~~~~~~i~~~l~~~ 25 (103)
|+-|..+....++.++|..||...
T Consensus 3 ~l~Y~S~~~~~~~~~~~~~Il~~s 26 (93)
T PF04940_consen 3 RLIYVSTASEDLSPEDLADILRSS 26 (93)
T ss_dssp EEEEEEEE-TTS-HHHHHHHHHHH
T ss_pred EEEEEEccCCCCCHHHHHHHHHHH
Confidence 788999999999999999999865
No 70
>PF03165 MH1: MH1 domain; InterPro: IPR003619 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3QSV_A 1MHD_A 1OZJ_A 3KMP_B.
Probab=20.37 E-value=84 Score=21.53 Aligned_cols=26 Identities=35% Similarity=0.497 Sum_probs=20.8
Q ss_pred HHHHHHHHhcCC--ChHHHhhhcCCCCc
Q 044925 34 KIATLIKLFEKR--SADELYLNVGSGGA 59 (103)
Q Consensus 34 kI~~li~aL~gk--~I~eLIa~v~agg~ 59 (103)
.+..|++.|+.+ .+++|+..+.+.|.
T Consensus 4 ~~~sLlkkLK~~~~~le~L~~Av~s~g~ 31 (103)
T PF03165_consen 4 AIKSLLKKLKKKIGQLEELLKAVESRGD 31 (103)
T ss_dssp HHHHHHHHHTTTCTHHHHHHHHHHCTTT
T ss_pred HHHHHHHHHccccchHHHHHHHHhcCCC
Confidence 478899999888 89999988775443
No 71
>PTZ00184 calmodulin; Provisional
Probab=20.36 E-value=1.1e+02 Score=20.02 Aligned_cols=30 Identities=10% Similarity=0.166 Sum_probs=25.2
Q ss_pred cCCchhhHhhhhhcccccccHHHHHHHHHHh
Q 044925 12 FWPHNTIDSGLVEFSFFTSQPEKIATLIKLF 42 (103)
Q Consensus 12 ~~~~~~i~~~l~~~g~vevdaekI~~li~aL 42 (103)
.++.+++.++|..+| +.++.+.+..++..+
T Consensus 100 ~i~~~e~~~~l~~~~-~~~~~~~~~~~~~~~ 129 (149)
T PTZ00184 100 FISAAELRHVMTNLG-EKLTDEEVDEMIREA 129 (149)
T ss_pred eEeHHHHHHHHHHHC-CCCCHHHHHHHHHhc
Confidence 478889999999998 888888888888765
No 72
>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins [].; PDB: 2G0C_A 3MOJ_B.
Probab=20.15 E-value=28 Score=21.78 Aligned_cols=28 Identities=14% Similarity=0.241 Sum_probs=18.0
Q ss_pred hhhhcccccccHHHHHHHHHHhcCCChH
Q 044925 21 GLVEFSFFTSQPEKIATLIKLFEKRSAD 48 (103)
Q Consensus 21 ~l~~~g~vevdaekI~~li~aL~gk~I~ 48 (103)
|...+.||++..+..+.+++.|++..+.
T Consensus 38 I~~~~S~vev~~~~a~~v~~~l~~~~~~ 65 (74)
T PF03880_consen 38 IFDNFSFVEVPEEVAEKVLEALNGKKIK 65 (74)
T ss_dssp E-SS-EEEEE-TT-HHHHHHHHTT--SS
T ss_pred EeeeEEEEEECHHHHHHHHHHhcCCCCC
Confidence 4566678899999999999999877654
Done!